The genome of the common baking and brewing yeast Saccharomyces cerevisiae continues to be the most completely sequenced and annotated of any eukaryotic organism. With this invaluable resource as a reference, several groups have begun to sequence, assemble and analyse the genomes of various relatives of S. cerevisiae. Such analyses have led to more accurate annotation of the reference genome, clearer evidence for which genes are genuine and which seem dubious, and a wealth of information on regulatory motifs. The amount of sequence data is considerable, and many more interesting observations are likely to emerge from secondary studies. This work describes two such discoveries. It has been determined that the regions immediately surrounding budding yeast centromeres are excessively divergent between the species, and highly polymorphic between strains. This occurs despite the obvious importance of centromeres in chromosome dynamics, and despite the absence of lengthy repetitious DNA that is characteristic of centromeres in other eukaryotes. As such it is a most unexpected finding, and although the mechanisms responsible for this 'supervariation' remain unclear it is sufficient to serve as a fingerprint for readily distinguishing many almost identical strains. It has also been established that a sizeable subtelomeric section of the S. cerevisiae genome has at some point in the past been horizontally transmitted (probably by hybrid introgression) to European strains of a wild relative Saccharomyces paradoxus. This is part of a growing body of evidence that there is extensive gene flow even between so-called species and that budding yeast genomes have a more complex and multi-layered history than previously anticipated.